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Sodium in PDB 6pul: Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru

Protein crystallography data

The structure of Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru, PDB code: 6pul was solved by W.Awad, A.N.Keller, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.49 / 1.84
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 216.548, 70.029, 143.252, 90.00, 104.30, 90.00
R / Rfree (%) 15.6 / 18.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru (pdb code 6pul). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru, PDB code: 6pul:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6pul

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Sodium binding site 1 out of 5 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:39.7
occ:0.80
 O E:HOH423 2.3 41.6 1.0
O E:TYR64 2.3 38.1 1.0
O E:HOH427 2.4 44.0 1.0
OH E:TYR47 2.5 43.8 1.0
O E:HOH482 2.5 45.3 1.0
O E:PRO61 2.6 44.7 1.0
C E:PRO61 3.5 45.7 1.0
C E:TYR64 3.5 40.1 1.0
CZ E:TYR47 3.5 40.2 1.0
CE2 E:TYR47 3.6 34.8 1.0
N E:TYR64 3.7 40.3 1.0
OD1 E:ASN65 4.0 39.3 0.4
N E:GLY63 4.1 45.1 1.0
CA E:ASN62 4.1 48.7 1.0
CB E:PRO61 4.1 42.6 1.0
CA E:TYR64 4.2 38.5 1.0
N E:ASN62 4.2 45.3 1.0
CA E:PRO61 4.3 39.5 1.0
NZ E:LYS57 4.3 68.3 1.0
C E:ASN62 4.5 49.3 1.0
CG E:ASN65 4.5 44.0 0.4
N E:ASN65 4.5 40.6 0.6
N E:ASN65 4.5 40.4 0.4
C E:GLY63 4.7 44.3 1.0
CA E:ASN65 4.8 40.5 0.6
CE1 E:TYR47 4.8 43.7 1.0
CB E:TYR64 4.8 35.3 1.0
ND2 E:ASN65 4.8 50.0 0.4
CA E:ASN65 4.8 40.5 0.4
OD1 E:ASN62 4.9 52.4 1.0
CA E:GLY63 5.0 45.9 1.0

Sodium binding site 2 out of 5 in 6pul

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Sodium binding site 2 out of 5 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na103

b:62.8
occ:1.00
 OH F:TYR78 2.6 51.6 1.0
O F:THR71 2.6 51.7 1.0
OD2 F:ASP76 2.6 55.5 1.0
CB F:ASP76 3.2 49.4 1.0
CG F:ASP76 3.3 54.3 1.0
CZ F:TYR78 3.5 47.1 1.0
N F:THR73 3.5 51.9 1.0
CE2 F:TYR78 3.5 42.6 1.0
CG2 F:THR73 3.6 59.4 1.0
OG1 F:THR73 3.6 56.2 1.0
O F:HOH294 3.6 53.1 1.0
C F:THR71 3.7 43.0 1.0
CA F:PRO72 3.8 46.3 1.0
C F:PRO72 3.9 49.7 1.0
CB F:THR73 4.0 60.0 1.0
CE F:LYS41 4.2 49.6 1.0
N F:PRO72 4.3 42.2 1.0
CA F:THR73 4.3 53.8 1.0
O F:HOH252 4.4 50.6 1.0
OD1 F:ASP76 4.5 56.1 1.0
NZ F:LYS41 4.5 50.3 1.0
CA F:ASP76 4.6 45.7 1.0
O F:PRO72 4.7 48.0 1.0
CE1 F:TYR78 4.8 43.1 1.0
O F:HOH277 4.8 50.0 1.0
CD2 F:TYR78 4.8 39.5 1.0
O F:HOH292 4.9 56.5 1.0
CA F:THR71 4.9 40.5 1.0
N F:THR71 4.9 45.0 1.0

Sodium binding site 3 out of 5 in 6pul

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Sodium binding site 3 out of 5 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na104

b:46.0
occ:1.00
 O F:LEU87 2.3 38.2 1.0
O F:HOH299 2.4 44.8 1.0
O F:HOH304 2.4 49.1 1.0
O F:HIS84 2.4 33.7 1.0
O F:HOH278 2.5 48.4 1.0
OD1 F:ASN83 2.5 40.0 1.0
C F:HIS84 3.4 36.0 1.0
CG F:ASN83 3.4 40.7 1.0
C F:LEU87 3.5 36.3 1.0
ND2 F:ASN83 3.8 46.6 1.0
N F:HIS84 3.9 32.7 1.0
CA F:VAL85 4.1 32.5 1.0
N F:LEU87 4.1 34.9 1.0
N F:VAL85 4.1 34.1 1.0
CA F:LEU87 4.2 32.4 1.0
CB F:LEU87 4.2 34.8 1.0
CA F:HIS84 4.3 31.9 1.0
C F:VAL85 4.3 35.4 1.0
O F:VAL85 4.4 35.0 1.0
O F:HOH343 4.5 69.9 1.0
N F:SER88 4.6 36.7 1.0
C F:SER88 4.7 38.5 1.0
CB F:ASN83 4.7 36.2 1.0
CA F:SER88 4.7 40.6 1.0
O F:HOH303 4.8 54.1 1.0
C F:ASN83 4.8 34.4 1.0
O F:SER88 4.9 44.1 1.0
N F:GLN89 5.0 37.7 1.0
CA F:ASN83 5.0 35.2 1.0

Sodium binding site 4 out of 5 in 6pul

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Sodium binding site 4 out of 5 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na302

b:39.0
occ:1.00
 O G:TYR64 2.4 35.5 1.0
O G:HOH510 2.5 38.1 1.0
O G:HOH524 2.5 44.2 1.0
O G:HOH498 2.5 39.2 1.0
OH G:TYR47 2.5 34.5 1.0
O G:PRO61 2.6 31.9 1.0
CZ G:TYR47 3.5 36.1 1.0
C G:PRO61 3.5 30.1 1.0
C G:TYR64 3.6 35.6 1.0
CE2 G:TYR47 3.7 34.2 1.0
N G:TYR64 3.9 34.6 1.0
CA G:ASN62 4.1 38.0 1.0
N G:GLY63 4.2 35.8 1.0
ND2 G:ASN65 4.2 43.6 0.7
CB G:PRO61 4.2 35.6 1.0
N G:ASN62 4.2 33.6 1.0
NZ G:LYS57 4.3 65.2 1.0
CA G:TYR64 4.3 29.7 1.0
CA G:PRO61 4.4 34.2 1.0
C G:ASN62 4.5 37.7 1.0
CG G:ASN65 4.5 48.8 0.7
O G:HOH682 4.6 40.0 1.0
N G:ASN65 4.6 35.4 1.0
OD1 G:ASN65 4.7 57.9 0.7
OD1 G:ASN62 4.8 39.9 1.0
CE1 G:TYR47 4.8 35.5 1.0
CA G:ASN65 4.8 37.1 0.3
CA G:ASN65 4.9 37.0 0.7
C G:GLY63 4.9 36.8 1.0
CB G:TYR64 5.0 29.5 1.0
CE G:LYS57 5.0 63.3 1.0

Sodium binding site 5 out of 5 in 6pul

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Sodium binding site 5 out of 5 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1 3'D-5-Op-Ru within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na501

b:70.2
occ:1.00
 O H:HOH660 2.4 61.7 1.0
O H:HOH657 2.5 63.3 1.0
O H:LEU87 2.5 64.1 1.0
O H:HOH656 2.6 73.5 1.0
O H:HIS84 2.6 56.1 1.0
OD1 H:ASN83 2.8 73.1 1.0
C H:HIS84 3.5 55.1 1.0
CG H:ASN83 3.6 73.1 1.0
C H:LEU87 3.7 64.0 1.0
ND2 H:ASN83 3.8 73.4 1.0
CA H:VAL85 4.0 54.8 1.0
N H:HIS84 4.2 51.6 1.0
N H:VAL85 4.2 50.3 1.0
N H:LEU87 4.2 52.9 1.0
C H:VAL85 4.3 58.9 1.0
O H:VAL85 4.3 60.1 1.0
CA H:LEU87 4.4 61.6 1.0
CA H:HIS84 4.5 52.5 1.0
CB H:LEU87 4.5 58.2 1.0
O H:HOH648 4.7 64.2 1.0
N H:SER88 4.8 68.2 1.0
O H:SER88 4.8 77.3 1.0
C H:SER88 4.9 74.8 1.0
CB H:ASN83 5.0 63.0 1.0
CA H:SER88 5.0 74.1 1.0

Reference:

W.Awad, A.N.Keller, J.Rossjohn. The Molecular Basis Underpinning the Potency and Specificity of Mait Cell Antigens To Be Published.
Page generated: Tue Oct 8 12:46:50 2024

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